Cyanine dyes are widely used as reagents for fluorescence labelling of biologically important molecules such as proteins, nucleic acids, hormones and drugs. Indeed, cyanine dyes offer a number of advantages over other fluorescent dyes. For example, the excitation and emission spectra of cyanine dyes span the visible and near-infrared spectrum from 450 nm to 800 nm. Furthermore, the cyanine dyes are characterised by having very high extinction coefficients and favourable quantum yields. See for example, U.S. Pat. Nos. 6,048,982, 5,268,486, 5,569,587, (Waggoner, A. S. et al). However, with certain cyanine dye structures there is a tendency towards self-association (or aggregation) leading to fluorescence quenching and a notable hypsochromic wavelength shift in absorbance.
Recently, Waggoner et al (Org. Letters, (2004), 6(6), 909-912) has described a polyfluoro-thiadicarbocyanine dye (i) having good photostability in aqueous solvents. The dye exhibited reduced aggregation, enhanced quantum yield and greater resistance to photobleaching when compared with a non-fluorinated analogue.

Modification of the indolinium ring of a carbocyanine dye at least one of the 3-positions, so as to introduce a reactive group or a conjugated substance has been described in WO 02/26891 (Molecular Probes Inc.). The modified dyes according to WO 02/26891 have also been reported to overcome the tendency of cyanine dyes to self-associate and dye conjugates labelled with the modified dyes are reported to be more fluorescent than conjugates labelled with structurally similar carbocyanine dyes.
Japanese Patent Application No. 5313304 (Fuji Photo Film Co. Ltd.) discloses a silver halide photographic sensitive material incorporating a dye containing multiple sulphonate groups and represented by formula (ii):
in which R10 and R11 may be alkyl carboxylate or alkyl sulphonate moieties and A includes:

Japanese Patent No. 61248789 (Ricoh KK) discloses an optical information recording medium including a recording layer containing a compound having the formula (iii):
in which A is represented by the formula:

Y is a halogen atom; a is an integer from 1 to 4; R1 and R2 are a C1-C5 alkyl group; R3 is a C1-C10 alkyl group which may be substituted by a sulphonyl group or a carboxyl group; R4 is hydrogen, halogen, amino or alkanoyloxy, Z is an atomic group necessary for the formation of a 4-8 membered ring, and m and n are integers from 0-3, where m+n≦3. Mader, O. et al (Bioconjugate Chem., (2004), 15, 70-78) describe the synthesis and photophysical properties of a series of pentamethine indocyanine dyes substituted at the aromatic ring positions with sulphonate, fluorine and methyl.
None of the above documents discloses reactive cyanine dyes and cyanine dyes conjugated to a substance, wherein the dyes contain at least one and preferably multiple fluoro substituents, as well as one or more sulphonic acid groups attached to the indolinium 1- and/or 3-positions of the cyanine chromophore.